International Tables for Crystallography (2012). Vol. F. ch. 18.4, pp. 485-498   | 1 | 2 |
https://doi.org/10.1107/97809553602060000858

Chapter 18.4. Refinement at atomic resolution

Contents

  • 18.4. Refinement at atomic resolution  (pp. 485-498) | html | pdf | chapter contents |
    Z. Dauter, G. N. Murshudov and K. S. Wilson
    • 18.4.1. The atomic model and a definition of atomic resolution  (pp. 485-487) | html | pdf |
      • 18.4.1.1. The atomic model  (p. 485) | html | pdf |
      • 18.4.1.2. What is `atomic resolution'?  (pp. 486-487) | html | pdf |
      • 18.4.1.3. A theoretical approach to `atomic resolution'  (p. 487) | html | pdf |
    • 18.4.2. Data  (pp. 487-488) | html | pdf |
      • 18.4.2.1. Data quality  (pp. 487-488) | html | pdf |
      • 18.4.2.2. Anisotropic scaling  (p. 488) | html | pdf |
    • 18.4.3. Computational algorithms and strategies  (pp. 488-489) | html | pdf |
      • 18.4.3.1. Classical least-squares refinement of small molecules  (p. 488) | html | pdf |
      • 18.4.3.2. Least-squares refinement of large structures  (pp. 488-489) | html | pdf |
      • 18.4.3.3. Fast Fourier transform  (p. 489) | html | pdf |
      • 18.4.3.4. Maximum likelihood  (p. 489) | html | pdf |
      • 18.4.3.5. Twinning  (p. 489) | html | pdf |
      • 18.4.3.6. Computer power  (p. 489) | html | pdf |
    • 18.4.4. Computational options and tactics  (pp. 489-491) | html | pdf |
      • 18.4.4.1. Use of F (amplitudes) or F2 (intensities)  (pp. 489-490) | html | pdf |
      • 18.4.4.2. Restraints on coordinates and ADPs  (p. 490) | html | pdf |
      • 18.4.4.3. Partial occupancy  (pp. 490-491) | html | pdf |
      • 18.4.4.4. Validation of extra parameters during the refinement process  (p. 491) | html | pdf |
    • 18.4.5. Features in the refined model  (pp. 491-495) | html | pdf |
      • 18.4.5.1. Hydrogen atoms  (pp. 491-492) | html | pdf |
      • 18.4.5.2. Anisotropic atomic displacement parameters  (p. 492) | html | pdf |
      • 18.4.5.3. Alternative conformations  (p. 492) | html | pdf |
      • 18.4.5.4. Ordered solvent water  (p. 493) | html | pdf |
      • 18.4.5.5. Automatic location of water sites  (p. 493) | html | pdf |
      • 18.4.5.6. Bulk solvent and the low-resolution reflections  (pp. 493-494) | html | pdf |
      • 18.4.5.7. Metal ions and other ligands in the solvent  (p. 494) | html | pdf |
      • 18.4.5.8. Deformation density  (pp. 494-495) | html | pdf |
    • 18.4.6. Quality assessment of the model  (p. 495) | html | pdf |
    • 18.4.7. Relation to biological chemistry   (pp. 495-496) | html | pdf |
    • 18.4.8. Practical strategies  (p. 496) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 18.4.1.1. The thermal-ellipsoid model used to represent anisotropic atomic displacement, with major axes indicated  (p. 485) | html | pdf |
      • Fig. 18.4.1.2. Histograms of B values for a protein structure, Micrococcus lysodecticus catalase (Murshudov et al., 1999), for two different crystals which diffracted to different limiting resolutions  (p. 487) | html | pdf |
      • Fig. 18.4.5.1. (a), (b) Representative electron-density maps for the refinement of Clostridium acidurici ferredoxin at 0.94 Å resolution (Dauter, Wilson et al., 1997)  (p. 491) | html | pdf |
      • Fig. 18.4.5.2. Schematic representation of the bulk-solvent models described in the text  (p. 494) | html | pdf |
    • Tables
      • Table 18.4.1.1. The parameters of an atomic model  (p. 485) | html | pdf |
      • Table 18.4.1.2. Features which can be seen in the electron density at different resolutions  (p. 486) | html | pdf |